You have to cut and weld.. and make sure everylast bit of rust is gone.. not even the slightest bit left.. or you will see rust back within a few months..
and bondo is crap.. it retains water and will cause more rust..

and you dont need to use any bondo on the welds.. you grind the welds down and smoth them out.. and if its just minor imperfections use primer and lots of sanding.. if you must use body filler, use fiberglass..